3I2S

Crystal structure of the hairpin ribozyme with a 2'OMe substrate and N1-deazaadenosine at position A10

• PDB DOI: https://doi.org/10.2210/pdb3I2S/pdb
• NAKB: 3I2S

• Classification: RNA
• Mutation(s): No 


• Deposited: 2009-06-29 Released: 2009-11-03 
• Deposition Author(s): Wedekind, J.E., Spitale, R.C., Krucinska, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.261 
• R-Value Work: 0.239 
• R-Value Observed: 0.239 

Starting Model: experimental

Literature

Single-atom imino substitutions at A9 and A10 reveal distinct effects on the fold and function of the hairpin ribozyme catalytic core.

Spitale, R.C., Volpini, R., Mungillo, M.V., Krucinska, J., Cristalli, G., Wedekind, J.E.

(2009) Biochemistry 48: 7777-7779

• PubMed: 19634899 
• DOI: https://doi.org/10.1021/bi9011622
• Primary Citation of Related Structures:  
  3I2Q, 3I2R, 3I2S, 3I2U


• PubMed Abstract: 
  

  The hairpin ribozyme cleaves a phosphodiester bond within a cognate substrate. Structural and biochemical data indicate the conserved A9 and A10 bases reside close to the scissile bond but make distinct contributions to catalysis. To investigate these residues, we replaced the imino moiety of each base with N1-deazaadenosine. This single-atom change resulted in an 8-fold loss in k(obs) for A9 and displacement of the base from the active site; no effects were observed for A10. We propose that the imino moiety of A9 promotes a key water-mediated contact that favors transition-state formation, which suggests an enhanced chemical repertoire for RNA.

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Organizational Affiliation: 

Department of Biochemistry & Biophysics, 601 Elmwood Avenue, Box 712, Rochester New York 14642, USA.

Biological Assembly 1  

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 20.54 kDa 
• Atom Count: 1,347 
• Modelled Residue Count: 62 
• Deposited Residue Count: 63 
• Unique nucleic acid chains: 2
• Unique hybrid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-R(*UP*CP*CP*CP*(A2M)P*GP*UP*CP*CP*AP*CP*CP*GP*U)-3'	A	14	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA/RNA (30-MER)	B	30	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
5'-R(*UP*CP*GP*UP*GP*GP*UP*AP*CP*AP*UP*UP*AP*CP*CP*UP*GP*CP*C)-3'	C	19	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NCO	E [auth B], F [auth B]	COBALT HEXAMMINE(III) Co H18 N6 DYLMFCCYOUSRTK-UHFFFAOYSA-N
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.261 
• R-Value Work: 0.239 
• R-Value Observed: 0.239 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.83	α = 90
b = 92.83	β = 90
c = 132.69	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-11-03 
Deposition Author(s): Wedekind, J.E., Spitale, R.C., Krucinska, J.

Revision History  

• Version 1.0: 2009-11-03
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description